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Yorodumi- PDB-6cba: Ethylene forming enzyme in complex with manganese, 2-oxoglutarate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cba | |||||||||
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Title | Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and canavanine | |||||||||
Components | 2-oxoglutarate-dependent ethylene/succinate-forming enzyme | |||||||||
Keywords | OXIDOREDUCTASE / manganese / 2-oxoglutarate / canavanine | |||||||||
Function / homology | Function and homology information 2-oxoglutarate dioxygenase (ethene-forming) / 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming) / 2-oxoglutarate oxygenase/decarboxylase (ethylene-forming) activity / ethylene biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Pseudomonas savastanoi pv. phaseolicola (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å | |||||||||
Authors | Fellner, M. / Martinez, S. / Hu, J. / Hausinger, R.P. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2024 Title: Structural, Spectroscopic, and Computational Insights from Canavanine-Bound and Two Catalytically Compromised Variants of the Ethylene-Forming Enzyme. Authors: Chatterjee, S. / Fellner, M. / Rankin, J. / Thomas, M.G. / J S Rifayee, S.B. / Christov, C.Z. / Hu, J. / Hausinger, R.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cba.cif.gz | 230.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cba.ent.gz | 184.7 KB | Display | PDB format |
PDBx/mmJSON format | 6cba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/6cba ftp://data.pdbj.org/pub/pdb/validation_reports/cb/6cba | HTTPS FTP |
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-Related structure data
Related structure data | 6cf3C 8uc2C 5v2zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39716.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas savastanoi pv. phaseolicola (bacteria) Gene: efe / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), EC: 1.14.11.34 |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-AKG / |
#4: Chemical | ChemComp-GGB / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.55 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.5 ul 64 mg/ml EFE (1 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, 3 mM canavanine, 2 mM 2-oxoglutarate) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir of 200 ...Details: 0.5 ul 64 mg/ml EFE (1 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, 3 mM canavanine, 2 mM 2-oxoglutarate) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir of 200 ul contained 25% w/v Polyethylene glycol 3,350, 0.1 M Bis-Tris pH 6.5, 0.2 M sodium chloride. The crystal was soaked for about a minute in 25% w/v Polyethylene glycol 400, 75% reservoir solution before freezing it. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9762 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.13→48.43 Å / Num. obs: 128283 / % possible obs: 98.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 9.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Rrim(I) all: 0.087 / Net I/σ(I): 11.3 / Num. measured all: 924312 / Scaling rejects: 1146 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V2Z Resolution: 1.13→32.491 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 16.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.74 Å2 / Biso mean: 16.374 Å2 / Biso min: 5.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.13→32.491 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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